Manhattan: Aftermath
by avngstories
Summary: Continues were "The Avengers" ended. Tony Stark, Steve Rogers, Thor, Bruce Banner, Clint Barton & Natasha Romanoff survived the battle, but now they have to face the aftermath. New York is in shambles and with a gag on Loki's lying mouth, truth starts popping out everywhere.
1. Chapter 1

_Iron Man falls from the sky. They realize he's not slowing down. Just in time, the Hulk catches him…but Stark is not moving. Hulk rips off his face mask. Rogers and Thor look at Stark's lifeless body and realize that even the light in his chest has gone out… the Hulk's sad bellow seems to shock Tony Stark back to life…_

The alien invasion of New York had been stopped. The devastation of Midtown Manhattan was nearly incomprehensible. Even as alien carcasses were still falling from the sky, people had begun to move. The National Guard and other first responders began tending to the most severely injured on the streets. More people streamed out of buildings and subway exits. Every military and civilian piece of equipment on the East Coast was already on its way to New York.

Agent Natasha Romanoff stood injured and dazed on the top of Stark Tower, Loki's scepter still in her hands. Dr. Selvig had collapsed. She checked to see if he was still alive, and satisfied that he was, she tried to contact the rest of her team. _Team_? A rather strange team, but Fury had been calling them that for so long that Natasha had the name stuck in her head.

"Romanoff here…" she questioned the air.

"Rogers here, we're on the ground. Stark is alive."

"Glad to hear it," she sighed out, "Barton, do you read me? What's your position?"

Silence.

The team on the ground looked at each other and realized they hadn't heard from Agent Barton in several minutes.

On the roof, Natasha frantically looked to the building position where she last saw him. That roof was no longer there.

She summoned all the strength she had left to call for him one more time, thinking that God or the universe, or whatever could not possibly be so cruel as to take him from her now. Now that she just got him back. "Barton?"

"I'm here. I- I'm somewhere in an office building – I think." He stuttered.

Natasha sat down, silently thanking God and the universe for sparing him again.

"Barton, can you move?" questioned Rogers.

"Not so much right now." Barton coughed out.

"I can find him." Offered Thor. He spun up his hammer and jumped away.

Clint was still trying to sit up, hoping that the dent in his body made by landing on his quiver would not be permanent when Thor jumped through a busted out wall of windows.

Clint managed to stand up and face Thor squarely. The guy was bigger than Clint remembered.

Clint could also still remember the rage Loki felt for his brother.

"So that asshole is your brother?" Clint asked him

Thor nodded - the pain obvious on his face.

"I had a brother. He went bad and I had to kill him."

Thor understood what Barton was telling him. Clearly when Barton had been overtaken by Loki, Barton realized that Loki could not be killed by humans.

"Perhaps my father can get through to him…" Thor said heavily.

Clint shook his head "so that's your plan? Take him back? For what? What do you people do to someone like Loki?"

"I don't know." Said Thor, as if he had already thought of every possibility and realized how each one wouldn't work.

Thor shook off his pain and decided to face the challenges of the moment.

"Let's get back to the others, archer." He grabbed Barton by the vest and jumped back out the window, Clint cursing all the way down.


	2. Chapter 2

Rogers was the first to recover.

"Where's Loki now?" he asked Thor.

"Hulk smash!" the big green guy growled.

They all spun to look at him, shocked beyond belief at hearing real words. Rogers thought he could see Banner's eyes somewhere behind the giant green face.

"Where?" asked Rogers?

The hulk pointed to what was left of the top of Stark tower.

"Ok, then let's go…"

The others followed along, everyone limping a bit, but with a new found rush of adrenaline at the thought of seeing what Loki looked like after his encounter with Hulk.

Entering Starks half destroyed penthouse they found Loki still in the hole in the concrete floor where Banner had left him – Natasha standing guard with the scepter.

When Natasha saw that Clint was with them, she dropped the godforsaken alien weapon and rushed over to him. They were both alive and standing, and a far as they were concerned everyone and everything else disappeared, if only for a minute. They stood there holding each other, propping each other up. Thor remembered what Loki had said to the woman while in his cell and realized the double meaning in Clint's previous words: _If I could, I'd kill him for you…_

Stark poked Loki with the foot of the Iron Man suit. Rogers motioned Stark to stop, but Stark just gave him '_a hey, it's fun' _kind of look. As soon as Loki stirred the rest rushed over. Loki, dazed from the epic beating from the Hulk, sat up to a face full of people who all had good reason to kill him.

"If it's all the same to you, I'll have the drink now." He said with an oily voice.

Thor promptly smashed the hammer into Loki's face, knocking him out once more. Thor pulled out what looked like alien handcuffs and secured Loki, drug him to a small room, and then planted his hammer on top of Loki, effectively pinning him to the floor. Then Thor pulled something else out of his belt, something his father had given him. It was a gag, a mask, something to keep Loki from talking and spreading his lies and deceit once and for all on this planet.


	3. Chapter 3

Thor walked back to the main room to join the others.

Rogers was concerned "Are you just going to leave him in there by himself?" demanded Steve.

"Yes, he can't move or speak." Said Thor.

"So what now?" asked Stark. "What do we do with reindeer games?"

Thor turned to face him, "I will have to take him back to Asgard to face our father."

Natasha turned to him as well "you think we're going to let you just take him?" she demanded. Just the effort of speaking drained whatever energy Natasha had left and she felt herself swaying a bit. She sat down on a step before she passed out in front of all these men.

"He has to." Clint said blankly, moving towards Natasha, having noticed her face-saving maneuver.

"He has to because Loki can't be killed here. And I promise you that he would find a way out prison, so this best plan is to send him back, where he can't hurt us anymore." By this time, Clint had reached Nat, and was sitting down beside her.

"Agreed." Said Stark.

"I agree too." Said Rogers.

Banner was still big and green, but sitting down. It wouldn't be long before he was back to himself. Stark grabbed a towel from the bar and tossed it Steve, indicating that Banner might need it soon.

Romanoff suddenly remembered poor Dr. Selvig passed out on the roof.

"Thor?" she asked wearily, "Selvig is still out there, can you get him to an ambulance on the ground?"

Thor rushed out the damaged window wall after his friend.

As the others talked, Natasha felt the adrenaline wearing off and became very aware she was a mere mortal, unlike some of the other people in the room. It was a good thing she had already made it to the floor, because she was sure the floor was going to be her final destination. She started breathing harder, trying to slow it down, but couldn't. The cold feeling of shock was starting to take over. Clint put his arm around her shoulder and whispered in her ear.

"You hit bad?

"No, just beat up all over." The effort of the speaking hurt.

Clint moved to check her pupils and pulse, becoming alarmed as the seconds ticked by.

"When was the last time you drank or ate anything?" he said lowly, in Russian.

"Not sure, a while." She mumbled back in Russian.

By this time the others had noticed Natasha starting to fail and move towards her. Clint put up hand to motion them back.

"It's ok, I've got her. She'll just get worse if you crowd her." He said, chastising them for not realizing that she really didn't these people her face right then.

"Stark," Clint barked, you got something other than alcohol in that bar? Anything with sugar? Juice, soda, anything? And water too!"

"Um, yeah, yeah." Stark jumped back and hurried to the bar. He rummaged for a second and came back with two small bottles – one with orange juice, one with water.

"Good, thanks." Said Clint, a little friendlier. He held the juice up to Natasha's lips.

"You have to drink this, Tasha."

She shook her head and leaned back, and would have fallen if Clint hadn't caught her. He held her in his arms. "Please, Nat, if you don't I'll call for a med evac, I swear I will."

The threat seemed to work, because Natasha reached for the juice, as Clint steadied her hand.

"Don't you think we should anyway?" started Rogers, "we should get the both of you out of here."

Clint shook his head "no, if I'm walking, I'll make it until the ground teams get here. Nat needs fluids first, then we'll asses her."

Natasha shook her head again, Clint continued, ignoring her "were kind of used to having to wait for medical attention." He sighed again and turned back to make sure Natasha was still drinking.

The other men in the room looked at Barton and Romanoff with a mixture of dismay and admiration.

Natasha knew she would puke for sure if she drank too fast, so she sat there, drinking slowly, willing herself to not pass out.

Clint looked at her with concern, "List 'em" he ordered.

"Left ankle got smashed on the carrier, right knee when I jumped on the flying motorcycle thing. Blow to the ribs somewhere, can't feel my right thumb, and assuming I have a concussion."

Stark was startled not only at her long list of injuries, but the matter of fact way in which she reported them.

Thor returned after having delivered the physicist to the ground and noticed the injured agents sitting on the floor. He wondered if he would need to transport them too…

"Your turn." She sighed.

"Well, there's the screaming headache from the demon possession and the 2 cracks on the head you gave me"…he said, putting hand up to his left ear…"they got me in the ribs too, landed on the bad shoulder when I went through the window." He rattled out in the same tone as Romanoff.

"Please tell me you're joking about the window?" she mumbled.

He gave her a wink, "sorry, not joking" He knew he'd half to face the music on that one later, but that Nat didn't have the energy to go after him right now.

Natasha just shook her head, but quickly regretted it. She felt the juice coming back up and reached for the water.

Someone in a corner coughed. It was Banner. Rogers, Stark, and Thor had been focusing on Barton and Romanoff and failed to notice that Banner was once again Bruce. Steve hurried over to toss him the towel.

Stark, not exactly feeling 100% himself stepped back to his platform and started the automated process of armor removal. He was glad to finally be free of it. To feel human again.

Stark walked back over the Banner, who was still on the floor, with nothing to wear but a towel.

"Go down the hall to the bedroom on the left. There are clothes in there." He nodded in the direction of his dressing room.

Banner got up, strategically arranging his towel as he did, and hurried off, really hoping that Agent Romanoff couldn't see his backside. He's scared her enough for one day.

Just then Fury's voice broke through on what was left of everyone's comm links.

"Status report NOW!" he bellowed.

Thor and Rogers jumped. Stark just rolled his eyes and looked annoyed. "Yeah, we're still alive, thanks for checking…" he jabbed.

Clint still had his right arm around Nat, but raised his left to stop Stark.

"Barton, here sir. Loki is secured. We got him."

"Where is everybody?"

"Top of Stark Tower sir. Everyone accounted for."

"Injuries?" Maria Hill's voice chimed in.

"Just Romanoff and me"

"Well, I figured that Barton. What injuries exactly?"

"Nothing that's going to kill us in the next hour."

"Good. Hold your position. We'll get to your within the hour." Replied Fury. Both Clint and Natasha heard the pause in Fury's voice. They exchanged glances, not sure which one of them had the courage to do it… Clint found his resolve first.

"How's Coulson?" he asked.


	4. Chapter 4

The pause seemed to last forever and Clint could have heard Hill's gasp even if she hadn't been on the comm.

"On life support." Came Fury's answer.

"Understood, Sir. Barton out."

Banner walked back in, clothed, and confused as to why Rogers and Stark were glaring at everyone else.

"What'd I miss this time?" he asked sheepishly.

Thor, not as clueless as everyone assumed, tried to diffuse the situation.

"News. Coulson was gravely injured by Loki, but your medicine people have kept him alive." Thor directed that statement more to Tony than anyone else. What the rest didn't understand was Thor was not shocked by the news. On his world it wasn't uncommon for someone to enter a deep sleep for a long time to recover from severe injuries.

"Oh," Banner said, not knowing what had happened on the carrier after he and Romanoff fell through the floor, causing him to change into the other guy.

Rogers looked confused and hurt. Stark moved to stand next to him.

"Told you Fury's lies have lies, Cap. Now do you believe me?"

The sting of Fury's ruse hit Rogers still harder. "W-why would he do that?"

"I'm sorry Steve, we had no choice." Romanoff said weakly, struggling to remember what language to speak. "We needed you to have a reason to work together."

He turned to her, "We?"

"Fury told the truth. The medics did call him, but then Fury took one of his own shots and injected it straight into Phil's heart. It bought them enough time to get him on life support." She strained at so many words.

Rogers wasn't exactly sure what that meant, but he had a suspicion. "But what about the cards?" asked Rogers.

Natasha looked down at the ground.

"That was your idea wasn't it?" Stark snapped. "And what the hell do you mean 'one of his own shots'?

"It was a serum shot wasn't it?" said Rogers flatly.

Both Romanoff and Barton nodded their heads.

Banner finally figured out what had gone down.

"You mean, so Fury, he's like Steve?" asked Banner, pointing to Rogers.

"No one is like Rogers," Barton replied. "You weren't the only one working on it Dr. Banner. After the war, they never really stopped. They never got it right though. I guess you know that?"

Banner nodded that he did indeed know.

"I really don't know all the details, but I suspect that Fury doesn't have a choice but to keep taking it…"

That statement made Stark take a step back. "Shit, that is surprising."

Natasha was feeling a bit stronger now as was able to speak more, "Stark, this whole thing was Coulson's job. My job. Barton's job. We were ordered to monitor threats and recruit and assemble a response team that has the ability to neutralize those threats. And we did that job. I'm not going to apologize for that."

Stark pointed at Romanoff, "You still lied." He jabbed.

"Really Stark? You're a hypocrite, you know that?"

"How's that Agent Romanoff?"

"You did exactly the same thing to your best friend."

Stark gave her a dirty look and walked away, knowing how right she was.

Despite hating being lied to, Rogers could appreciate Romanoff's commitment to completing her mission. He wasn't sure what Romanoff and Stark were talking about, and didn't really care right then anyway. He'd find out later.

Banner and Thor just stood there, not sure what to say.

Stark spun around again "Well, is he going to make it? Is Phil going to be OK?" he said with a pained looked, remembering how good Phil had been to him and Pepper, especially Pepper.

"I don't know…" she was shaking from the shock and from the thought of Phil not making it. Clint held her tighter.

"We done now?" Clint growled back to Stark.

"Yeah, we're done." Conceded Stark. "Wait" Tony Stark was never really done talking, "I never said thank you, Agent Romanoff."

"What?" she mumbled.

"For what you did that night, taking care of Pepper, making sure everyone got out, tracking me down, injecting me with poison, all of it." he waved.

Now Steve was sure he'd have to ask about the story later…

Tony nodded to Barton, "Were you there too that night?"

"Yeah", was all Clint would say.

"Thanks." Replied Tony.

_More chapters to follow…_


	5. Chapter 5

Stark continued on, "So, I was promised shwarma for not dying, what do you say let's go find it?"

"Huh?" asked Barton bewildered.

"Yes, we did promise him food, Barton." Said Rogers almost apologetically.

Clint turned to Nat and checked her pupils and pulse again, "you need to eat" he said quietly in Russian.

Natasha didn't have the strength to argue anymore.

By this time Banner and Thor were sitting on the couch watching the conversation, both not sure what was going on. Bruce wondered what in the world Stark had done to make Romanoff inject him with poison.

Barton got up and carefully pulled Natasha to her feet, steadying her a bit. Steve moved forward to help, but got an icy look from Romanoff. Apparently, Barton's help was enough for her.

Barton looked at them all, "Well we have 51 minutes before we have to be back here. Thor, are you sure Loki is secure?"

Thor rose up off the couch, "I will check on him." He sighed. "Be-Banner, can you assist me?" Thor wanted the beast by his side just in case Loki had recovered.

"Uh, sure." Banner said, following Thor. Somehow Bruce just couldn't get the phrase _'puny god'_ out of his head. It made him smile a little.

Rogers was still not sure how in the world Barton and Romanoff were able to walk to the elevator under their own power, but he noticed how they seemed to draw strength from each other. Neither able to do it on their own, but somehow able to do it by holding on to the other.

Steve turned to Stark, "Well this was your request…"

"Be right there, Cap, just trying to find Pepper and let her know I'm ok." he said, a phone at his ear.

"Oh." Steve nodded, assuming Pepper was someone very important to Stark. Wife? Girlfriend?

"Loki is still unconscious and secure, I assure you!" he boomed as he and Banner walked back out of Loki's makeshift prison cell.

Tony, on the phone and now arguing with Pepper about how he had tried to call her, but she didn't answer and so on- walked up to Thor and Banner motioning them to hurry up.

"49 minutes, let go!"


	6. Chapter 6

With 29 minutes to go until their extraction, the curious looking group sat silently in the damaged diner, slowly eating.

Steve was already starting to feel the need to sleep and heal. He hoped the others didn't think he was rude, but sleep was how he healed best…

Thor was fine and enjoying the food. He liked the food here. But really he was just stalling, avoiding having to go back and face Loki again. Trying, trying so hard to understand why Loki had done this…

Tony, for once, was quiet. He missed Pepper, couldn't wait until she could get back. He just wanted to hold her again and tell her everything was going to be ok…

Bruce was still a little disoriented from being the other guy for so long. Images flashed through his head, not memories so much as momentary pictures in his head. Thoughts of flying through air, hitting things – lots of things. Was there a giant alien whale? No, that couldn't be right…

Natasha and Clint were worse off. Natasha had to steady herself in her chair and force herself to eat a few small bites. Clint sat next to her, his leg on her chair, propping her up from behind. Clint made sure his left side was facing away from the group. All the electromagnetic shit flying through air during the battle had fried all but one half of his last set of aids. But no one was talking anyway. _Small mercies_, thought Clint.

Clint was still focusing on Natasha, making sure she was ok, when he noticed her starting to sway again.

"What's your name?" _in Russian_

"Natasha Romanoff" _in English_ – giving him a dirty look but answering anyway..

"What day is it" _in Spanish_

"Tuesday," _in Spanish_. The answer was supposed to be in English

"What city are we in" _in Arabic_ – that was a trick because they were in a swarma joint

"N-New York?" she stumbled a bit but made it to English

Tony shot a look to Bruce "What's that all about?"

"I think he's checking the severity of her concussion."

Thor leaned forward "Is she alright?"

Bruce shook his head no. Stark started to look worried – fidgeting a bit before Bruce motioned him to be quiet.

Clint still was still probing Natasha in a few more languages …

"What's my name" his asked.

"Shithead" this time in English. They both smiled a little

Tony piped in "Well, did she pass the test?"

Clint shook his head, "she missed 4 out of 10"

"Is that bad" asked Steve, no one had noticed him wake up.

"Could be better" Clint said, not joking this time.

"I'll make it." she muttered.

"She's a fierce little warrior." Said Thor in admiration.

Natasha shot Thor the dirtiest look. That made Clint smile a little again.

He leaned forward, grabbed her wrist without asking, and checked her pulse again. He studied her eyes.

"Right one's a little blown Tasha" he said with concern.

"How many minutes?"

"7" he replied, hoping it would be sooner.

Clint got up out of his chair, favoring his knee, and carefully coaxed Natasha to sit on the floor. He held her in his lap, keeping her head up. Clint didn't want her falling out of the chair if she passed out.

"Just need to close my eyes a minute." She mumbled.

"Uh, uh, no you don't", he said shaking her carefully; "eyes open Tasha!"

She tried her best to stay awake.

The other men at the table grew more agitated.

"Why don't I go outside and wait for them?" asked Steve.

Stark looked nervous, biting his lip to hold back any of his snarky comments. He just kept thinking how tough these too were and they had no armor like him, no genetic enhancements like Steve and Bruce, and they definitely were not immortal aliens. What in the hell had these two been through to make them this damn tough? Tony wasn't sure he wanted to know. It was almost like they had been prepared for this. No, that couldn't be it, could it? They were just a really good soldier and super talented spy, right. And a couple too, that much was clear.

Starks thoughts were interrupted by a wave of SHILED people sweeping in the door - Rogers caught in the middle of them, Fury at the back.

Medics rushed over to Barton and Romanoff, one of them carefully pulling them apart, like she'd done it before. Four guards took position in the restaurant, two each clearly focused on Thor and Banner.

Fury just nodded to Stark, as if telling him that Tony could say his peace later but now was not the time.

Fury walked over to his agents and knelt down, his hand on Barton's shoulder.

"Good work, you two." He said with more genuine emotion than Stark had ever seen the man in black display.

Clint nodded clumsily; Natasha was being lifted onto a stretcher. Clint reached for her as the medics carried her away. Fury held him back gently.

"They've got her, it's ok." fury said quietly.

Fury swallowed hard when Barton didn't respond. He bent closer, making sure Clint could see him talking…

"It's ok, son, it's over. We won."

Rogers noticed the sincerity in Fury's voice. This was a version of Nick Fury Rogers had never seen. It was if all the pretense, all the half-true stories, all the bigger than life aura of Nick Fury had been peeled back. Steve could see the older man's concern, his affection, and his pride. Clint Barton lay down on the floor, and closed his eyes. More medics rushed over, assuming Barton had passed out. Rogers realized Clint hadn't collapsed, just laid down to rest.

Fury stood up and faced Rogers, Thor, Stark, and Banner.

The medics loaded Clint on a stretcher anyway and headed for the evac chopper.

The other Nick Fury had returned. "Cap, Thor, Stark, Dr. Banner, thank you." He bowed a little to them in gratitude and turned to walk out the door. "Now take me to Loki." And he walked out the door; the expectation that the other 4 would follow him was obvious. Stark caught up to Fury.

"Hey?" Stark asked "is that unholy love child of Robert Ludlum and Nicholas Sparks going to be ok?" pointing to Romanoff and Barton being secured in a medical helicopter.

"Not their worst mission." Fury said, shaking his head. "Now where is that horned sonofabitch?"


	7. Chapter 7

Fury, his guards, and Thor found Loki right were Thor had left him. Fury was impressed with the handcuffs and gag- especially the gag.

Fury turned to Thor, "So NOW what?" he asked the asgardian?

"He cannot be held here or killed here for that matter." Said Thor, still hoping the killed part was avoidable.

"Well why NOT?" demanded Fury.

"Loki's kind cannot be killed by your kind." Say Thor blankly. "The can only be killed by my kind." He continued, sadly.

"So how do you take him back?" asked Fury, already suspecting the answer.

"The tesseract is the only way." Replied Thor.

"So that means if we want to lose Loki we have to lose it too?"

"Yes." Said Thor firmly.

"Understood." Said Fury, almost relieved that the damn blue cube was finally going to be gone for good. Ever since the Nazi's had uncovered it the '30's the thing had been causing death and war for whoever had tried to harness its energy.

"Keep Loki here a while more. I want see him pinned under that hammer until he begs for mercy. Can you do that?"

"I can. And I will." Said Thor.


	8. Chapter 8

The next morning, Natasha woke up in the infirmary, an IV in her hand, her ankle wrapped and elevated, and ribs wrapped. Clint was still asleep on cot next to her bed. His IV had been removed during the night. Natasha tried to sit up, but the pain in her head reminded her to lie back down. Her movement woke Clint, who looked up at her with blood shot eyes.

"You ok?" he asked.

Natasha just groaned. "You?" she managed to say.

"Nat, did we just fight an alien invasion?"

"Think so."

"Uhhg!" he moaned and flopped back down.

A nurse heard them talking and popped her head in the door, "Stay DOWN! Agents." She ordered.

Clint raised his hand to her, "No problem." And dropped his arm back down like it didn't work anymore.

They were both asleep again in a few seconds.

Two days passed before Loki even regained conscience, but he was still unrepentant. Thor could wait. Their people experienced time differently.

In that time, Barton and Romanoff were discharged from the hospital with strict orders to stay on the SHIELD base in New York. Before they left the medical wing, they were allowed to see Phil Coulson. His condition was unchanged, and Natasha sobbed into Clint's shoulder at the sight of Phil being kept alive by machines. No one knew how long Phil would stay that way.

New York was still reeling in the aftermath. Reality had been changed. Every in the world now knew that humans were not alone in the universe and speculation as to what the future held was everywhere. The news media had latched onto the public's fascination with Iron Man, Captain America, and Thor. People were divided as to whether the big green monster came from outer space or not. Some people claimed he had been seen years before, but others found that hard to believe. Thankfully for SHIELD, its agents had managed to go un-filmed, save for one shot of a man dressed in black carrying a child out of bus window. That shot was Nick Fury's personal favorite.

Tony Stark and Steve Rogers were used to the attention, so they kept out in public so as keep the focus away from the other fighters. Bruce Banner stayed in Stark Tower with Thor, as much to hide out as to keep an eye on Loki. The helicarrier crew was overwhelmed with repairs and poor Maria Hill hadn't slept in days, for fear that something else on the carrier would break and cause the ship to sink. It would be months before it could fly again. Fury divided his time between the damaged carrier and the New York base, spending more time in his helicopter surveying the damaged city than anywhere else. He'd been called to Washington D.C. 12 hours prior, but kept giving them excuses as to why he couldn't possibly leave New York.

_More chapters coming soon…_


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